Alexa488
A water soluble fluorescent dye used for protein and nucleic acid labeling. It is excited at a wavelength of 488 nm.Link: Alexa488 on Wikipedia.

Alexa555
A water soluble fluorescent dye used for protein and nucleic acid labeling. It is excited at a wavelength of 555 nm.Link: Alexa555 on Wikipedia.

aliquot
A small portion. It is common practice to subdivide a precious solution of reagent into aliquots that are used when needed without handling the total sample. (CancerWEB)A known amount of a homogeneous material, assumed to be taken with negligible sampling error. The term is usually applied to fluids. The term "aliquot" is usually used when the fractional part is an exact divisor of the whole; the term "aliquant" has been used when the fractional part is not an exact divisor of the whole (e.g. a 15 mL portion is an aliquant of 100 mL). When a laboratory sample or test sample is aliquoted or otherwise subdivided, the portions have been called split samples. (IUPAC Compendium of Chemical Terminology)

aromaticity
Aromaticity is a chemical property in which a conjugated ring of unsaturated bonds, lone pairs, or empty orbitals exhibit a stabilization stronger than would be expected by the stabilization of conjugation alone. (Wikipedia.org)Link: Aromaticity on Wikipedia.

C-terminal end
The C-terminal end of a protein or polypeptide is the extremity of the amino acid chain terminated by a free carboxyl group (-COOH). Each amino acid has a carboxyl group and an amine group, and amino acids link to one another to form a chain by a dehydration reaction by joining the amine group of one amino acid to the carboxyl group of the next. Thus polypeptide chains have an end with an unbound carboxyl group, the C-terminus, and an end with an amine group, the N-terminus.Link: Wikipedia.org

Caged compounds
Compounds that release the effector species generally on a millisecond or faster time scale, upon flash photolysis with near-UV light. They are used principally in studies of rapid biological processes to enable the application of a bioeffector species at or near its site of action.Link: National Institute for Medical Research

carcinogenesis
The generation of cancer from normal cells, correctly the formation of a carcinoma from epithelial cells, but often used synonymously with transformation, tumourigenesis. (CancerWEB)

Characteristic Modulating Frequency
For a trap that is being modulated, being turned on and off, the characteristic modulating frequency achieves 63% of the trap stiffness possible for a continuous trap of the same power.

chloroform
A clear, colorless, heavy, sweet-smelling liquid, CHCl3, used in refrigerants, propellants, and resins, as a solvent, and sometimes as an anesthetic. Chloroform, once widely used in human and veterinary surgery, has generally been replaced by less toxic, more easily controlled agents. (Dictionary.com)The structure of chloroform.Link: Chloroform on Wikipedia.

Dark box
The part of the optical trap set up that contains the equipment that detects fluorescence

denaturation
To cause the paired strands of (double-stranded DNA) to separate into individual single strands. (Dictionary.com)To cause the tertiary structure of (a protein) to unfold, as with heat, alkali, or acid, so that some of its original properties, especially its biological activity, are diminished or eliminated. (Dictionary.com)Link: Denaturation on Wikipedia.

Denature
To induce structural alterations that disrupt the biological activity of a molecule. Often refers to breaking hydrogen bonds between base pairs in double-stranded nucleic acid molecules to produce in single-stranded polynucleotides or altering the secondary and tertiary structure of a protein, destroying its activity.Link: CancerWEB

Dichroic Mirror
Optic that transmits certain wavelengths and transmits others. For example, one of the dichoric mirrors used in the Lang group setup transmits visible light but reflects near-infrared light

Dipole
A pair of equal and opposite electric charges or magnetic poles separated by a small distance.

DNA
Deoxyribonucleic Acid. This is the genetic material that encodes for proteins and conducts various cellular functions in a living organisms.

Domain
An element of overall structure that is self-stabilizing and often folds independently of the rest of the protein chain. Most domains can be classified into "folds". Domains often are named and singled out because they play an important role in the biological function of the protein they belong to; for example, the "calcium-binding" domain of calmodulin.Link: Wikipedia.org

Duty Cycle
The fraction of time during which the laser is being operated. It is defined as the ratio of the laser pulse duration to the wave period. The wave period is defined as the amount of time it takes for a full wave to pass a specific point. The pulse duration is the amount of time that the laser is turned on. Therefore, for a laser that has a period of 0.5 microseconds and a pulse duration of 0.25 microseconds, the duty cycle is 50%.

E. coli
A species of rod-shaped, facultatively anaerobic bacteria in the large intestine of humans and other animals, sometimes pathogenic.Link: Dictionary.com

Equipartition Theorem
A principle of statistical mechanics. It states that the internal energy of a system composed of a large number of particles at thermal equilibrium will distribute itself evenly among each of the quadratic degrees of freedom allowed to the particles of the system. (wikipedia.org). In their paper, the Lang group used this theorem to determine the stiffness of their optical trap.

ethanol (EtOH)
A colorless volatile flammable liquid, C2H5OH, synthesized or obtained by fermentation of sugars and starches and widely used, either pure or denatured, as a solvent and in drugs, cleaning solutions, explosives, and intoxicating beverages. (Dictionary.com)The structure of ethanol.Link: Ethanol on Wikipedia.

etiology
A branch of knowledge concerned with the causes of particular phenomena, specifically a branch of medical science concerned with the causes and origins of diseases. (CancerWEB)Link: Etiology on Wikipedia.

extraction
A technique for separating components in a mixture that have different solubilities. For example, caffeine can be separated from coffee beans by washing the beans with supercritical fluid carbon dioxide; the caffeine dissolves in the carbon dioxide but flavor compounds do not. Vanillin can be extracted from vanilla beans by shaking the beans with an organic solvent, like ethanol. (General Chemistry Online!, Frostburg State University)

furan
One of a group of colorless, volatile, heterocyclic organic compounds containing a ring of four carbon atoms and one oxygen atom, obtained from wood oils and used in the synthesis of furfural and other organic compounds. (Dictionary.com)The structure of furan.Link: Furan on Wikipedia.

gene expression
Conversion of the information encoded in a gene first into messenger RNA and then to a protein. (Dictionary.com)The full use of the information in a gene via transcription and translation leading to production of a protein and hence the appearance of the phenotype determined by that gene. Gene expression is assumed to be controlled at various points in the sequence leading to protein synthesis and this control is thought to be the major determinant of cellular differentiation in eukaryotes. (CancerWEB)Link: Gene expression on Wikipedia.

Gene knockout
A genetically engineered organism that carries one or more genes in its chromosomes that have been made inoperative (have been "knocked out" of the organism). Link: Wikipedia.org

glycoside
Any compound that contains a carbohydrate molecule (sugar), particularly any such natural product in plants, convertible, by hydrolytic cleavage, into sugar and a nonsugar component (aglycone) and named specifically for the sugar contained, as glucoside (glucose), pentoside (pentose), fructoside (fructose) etc. (CancerWEB)

hemiacetal
A hemiacetal is a chemical structure with the general structure shown in the figure. Hemiacetal means "half acetal" and it refers to the fact that hemiacetals, instead of a second alkoxy (RO) substituent, have a hydroxyl (HO) substituent.The general structure of a hemiacetal.Link: Much more information on hemiacetals and acetals.See also: acetal

hydrolysate
The product of a hydrolysis reaction. Hydrolysates are generally named according to what reactant was hydrolysed to come up with the product, for example protein hydrolysate if the reactant was a protein. (CancerWEB)

metabolism
The sum of all the physical and chemical processes by which living organised substance is produced and maintained (anabolism) and also the transformation by which energy is made available for the uses of the organism (catabolism). (CancerWEB)Link: Metabolism on Wikipedia.

Microinjection
The process of using a micro needle to insert substances at a microscopic or borderline macroscopic level into a single living cell. It is a simple mechanical process in which an extremely fine micro needle penetrates the cell membrane and sometimes the nuclear envelope and releases its contents. Link: Wikipedia.org

microsome
Artefactual spherical particle, not present in the living cell, derived from pieces of the endoplasmic reticulum present in homogenates of tissues or cells: microsomes sediment from such homogenates when centrifuged at 106 g and higher: the microsomal fraction obtained in this way is often used as a source of mono-oxygenase enzymes. (IUPAC Compendium of Chemical Terminology)

Modulation Frequency
The instances per second that the laser beam hits the object under investigation

Momentum
In physics, the property or tendency of a moving object to continue moving. For an object moving in a line, the momentum is the mass of the object multiplied by its velocity (linear momentum); thus, a slowly moving, very massive body and a rapidly moving, light body can have the same momentum.

MWCO
Abbreviation for Molecular Weight Cut Off. Dialysis membrane pore sizes are characterized by the molecular weight at which 90% of the solute will be retained (prevented from permeating) by the membrane. Link: Spectrapor.com

Native chemical ligation
A common form of chemical ligation, a technique for constructing a large peptide from two or more smaller peptides. In native chemical ligation a peptide containing a C-terminal thioester reacts with another peptide containing an N-terminal cysteine, in the presence of an exogenous thiol catalyst. In a thermodynamically-controlled, freely reversible first step a transthioesterification occurs. The product rearranges irreversibly under the usual reaction conditions to form the desired amide bond. The process was developed by Phillip Dawson and Stephen Kent at The Scripps Research Institute in 1994.Native chemical ligation.Link: Wikipedia.org

Newtons
The SI unit of force, equal to the force that produces an acceleration of one meter per second per second on a mass of one kilogram.

nicotinamide adenine dinucleotide phosphate (NADP)
Nicotinamide adenine dinucleotide phosphate. A coenzyme composed of ribosylnicotinamide 5'-phosphate (nmn) coupled by pyrophosphate linkage to the 5'-phosphate adenosine 2',5'-bisphosphate. It serves as an electron carrier in a number of reactions, being alternately oxidised (NADP+) and reduced (NADPH). (CancerWEB)Link: NADP on Wikipedia.

nucleic acid
Any of a group of complex compounds found in all living cells and viruses, composed of purines, pyrimidines, carbohydrates, and phosphoric acid. Nucleic acids in the form of DNA and RNA control cellular function and heredity. (Dictionary.com)Link: Nucleic acid on Wikipedia.

Nucleotide
Any of a group of molecules that, when linked together, form the building blocks of DNA or RNA: composed of a phosphate group, the bases adenine, cytosine, guanine, and thymine, and a pentose sugar, in RNA the thymine base being replaced by uracil.

Numerical Aperture
A dimensionless number that characterizes the range of angles over which the system can accept or emit light.

Objective Lens
The part of the microscope in the optical trap that magnifies the specimen and focuses laser beams on it.

phenobarbital
A crystalline barbiturate used as a sedative, a hypnotic, and an anticonvulsant. (Dictionary.com)The structure of phenobarbital.

phenol
A caustic, poisonous, white crystalline compound, C6H5OH, derived from benzene and used in resins, plastics, and pharmaceuticals and in dilute form as a disinfectant and antiseptic. Also called carbolic acid. (Dictionary.com)The structure of phenol.Link: Phenol on Wikipedia.

Phosphate buffered saline
A buffer solution commonly used in biochemistry. It is a salty solution containing sodium chloride, sodium phosphate and potassium phosphate. The buffer helps to maintain a constant pH. The concentration usually matches the human body (isotonic)Link: Wikipedia.org

Phosphorylation
The addition of a phosphate group to an organic molecule. Phosphorylation is important for many processes in living cells. ATP is formed during cell respiration from ADP by phosphorylation , as in the mitochondria of eukaryotic cells (oxidative phosphorylation) and the chloroplasts of plant cells (photosynthetic phosphorylation). Phosphorylation also regulates the activity of proteins, such as enzymes, which are often activated by the addition of a phosphate group and deactivated by its removal (called dephosphorylation).Link: American Heritage Science Dictionary

Photobleach
To lose colour or make white by the action of light; e.g., the use of a laser to bleach a fluorescent dye covalently linked to a macromolecule.

Photolabile
A chemical that is easily dissociated by the absorption of light, usually in the visible or ultraviolet region. An example of a photolabile species is nitrous acid, HONO, which has a very short lifetime in sunlight.Link: Glossary of Meterology

Photon
The subatomic particle that carries the electromagnetic force and is the quantum of electromagnetic radiation. The photon has a rest mass of zero, but has measurable momentum, exhibits deflection by a gravitational field, and can exert a force. It has no electric charge, has an indefinitely long lifetime, and is its own antiparticle.

Pull-down assay
Also known as co-immunoprecipitation. Immunoprecipitation is the technique of precipitating an antigen out of solution using an antibody specific to that antigen. Can identify protein complexes present in cell extracts: by IPing one protein believed to be in a complex, additional members of the complex can also be identified.Link: Wikipedia.org

purine
A heterocyclic compound with a fused pyrimidine/imidazole ring. Planar and aromatic in character. The parent compound for the purine bases of nucleic acids. (CancerWEB)Link: Purine on Wikipedia.

pyrimidine
A family of 6-membered heterocyclic compounds occurring in nature in a wide variety of forms. They are planar and aromatic in character and include several nucleic acid constituents (cytosine, thymine, and uracil) and form the basic structure of the barbiturates. It is the parent compound of the pyrimidine bases of nucleic acid. (CancerWEB)Link: Pyrimidine on Wikipedia.

Refractive Force
The force component of the light beam in an optical trap that pushes the targeted object towards the center of the trap.

Refractive Index
The ratio of the velocity of light in a vacuum to that in a medium.

Residue
A single unit within a polymer, such as an amino acid within a polypeptide or protein.Link: CancerWEB

RNA interference
A mechanism for RNA-guided regulation of gene expression that is common in eukaryotic cells. RNAi involves double-stranded ribonucleic acid (dsRNA) interfering with the expression of genes with sequences that are complementary to this dsRNA. Link: Wikipedia.org

SAPD
Silicone Avalanche Photo Diode. A device that detects photons and measures the fluorescence of the specimen. In the paper it was used to measure the fluorescence decay of the Cy3 dye.

Scattering Force
The force component of the light beam in an optical trap that pushes the targeted object in the direction of light propagation

Schiff base
Any of a class of bases of the general formula R2C=NR that are obtained typically by condensation of an aldehyde or ketone with a primary amine (as aniline) with elimination of water, that usually polymerize readily if made from aliphatic aldehydes, and that are used chiefly as intermediates in organic synthesis and in some cases as dyes Schiff, Hugo Josef (1834-1915), German chemist. In 1864 Schiff discovered the condensation products of aldehydes and amines; the products are now known as Schiff bases. Two years later he introduced a test for aldehydes, in which decolorized fuchsin regains its color in the presence of aldehydes. (Dictionary.com)The general structure of Schiff bases (imines).

Semisynthesis
Building a complex compound from precursor molecules that are too structurally complex, too costly or too inefficient to be produced by total synthesis.Link: Wikipedia.org

Site-directed mutagenesis
A molecular biology technique in which a mutation is created at a defined site in a DNA molecule, usually a circular molecule known as a plasmid.Link: Wikipedia.org

sodium dodecyl sulfate (SDS)
The crystalline sodium salt C12H25NaO4S of sulfated lauryl alcohol; also : a mixture of sulfates of sodium consisting principally of this salt and used as a detergent, wetting, and emulsifying agent (as in toothpastes, ointments, and shampoos). (Dictionary.com)The structure of SDS.Link: SDS on Wikipedia.

Solid phase peptide synthesis (SPPS)
Process which allows the synthesis of natural peptides which are difficult to express in bacteria, the incorporation of unnatural amino acids, peptide/protein backbone modification, and the synthesis of D-proteins, which consist of D-amino acids. Unlike ribosome protein synthesis, solid-phase peptide synthesis proceeds in a C-terminal to N-terminal fashion. The N-termini of amino acid monomers is protected by these two groups and added onto a deprotected amino acid chain.Link: Wikipedia.orgLink: SPPS on Sigma-Aldrich

Spectroscopy
The branch of science devoted to discovering the chemical composition of materials by looking at the light (and other kinds of electromagnetic radiation) they emit.

Thioester
Compound resulting from the bonding of sulfur with an acyl group with the general formula R-S-CO-R'. They are the product of esterification between a carboxylic acid and a thiol (as opposed to an alcohol in regular esters). Link: Wikipedia.org